I wonder did you get the phosphorylated patch work stand alone? The ser_phosphorylated.txt cannot be called by using -patch_selectors since it doesn’t has CMDLINE_SELECTOR inside that. So the question now is how to use ser_phophorylated.txt patch. Anyone?
Have you tested whether your pdb has the ser_phosphorylated.txt patch created? Also, since this ser_phosphorylated.txt patch is to be read by Rosetta in default, you don’t need to specify that using -patch_selectors as you used for replonly.